The city is named after Nathan Boynton, a Civil War major and Michigan politician who became one of the first settlers in the area in 1895.

Native Americans inhabited modern-day Boynton Beach thousands of years ago, with a burial mound west of the city including artifacts dating as far back as roughly 150 BCE.

Byrd and Fred Dewey filed the original plat for the Town of Boynton in 1898, although official incorporation did not occur until 1920.

Boynton Beach's population grew rapidly in the first few decades following World War II, with more than a three-fold increase in the 1950s, while development of the city expanded westward, particularly in the 1980s.

Archaeological evidence indicates Native American inhabitation of the region dating back thousands of years, with Ais, Calusas, Jaegas, Mayaimis, and Tequesta settling in or near modern-day Palm Beach County.

[4] A complex of mounds west of present-day Boynton Beach and near the Loxahatchee National Wildlife Refuge includes shards of pottery possibly from 150 BCE.

[5]: 10–11 Captain James A. Armour, head keeper of the Jupiter Inlet Lighthouse, filed the first land claim in modern-day Boynton Beach in 1875, although it is unlikely he lived there.

[5]: 13  He was so impressed by the natural beauty of the year-round sunshine and pristine beaches, he built the famous Boynton Hotel, where he also spent winters with his family.

Pineapples, tomatoes, mangoes, and citrus fruit were packed in crates and shipped across the country on the newly built Florida East Coast Railroad.

Alonzo King and Samuel Cade, both African American farmers, taught these early settlers methods for cultivating muck soil and dealing with the presence of mosquitos and rattlesnakes.

[8] Fred S. Dewey, one of Flager's secretaries, bought a large area of land west of the Intracoastal Waterway earlier that year.

[5]: 17 A wood-frame schoolhouse opened in 1900 at Ocean Avenue and Seacrest Boulevard, replacing a smaller, temporary building.

[5]: 25  This building is listed on the National Register of Historic Places and was converted into the Schoolhouse Children's Museum & Learning Center in 2001.

[5]: 26  Shortly before the incorporation of Boynton, the 1920 census recorded a population of 671 people in Palm Beach County's fourth precinct, which also included Hypoluxo and the area that now comprises Ocean Ridge.

In 1921, the Town of Boynton acquired the beach site from Lewis S. Howe by eminent domain for park and recreation purposes.

In 2011 the boardwalk was renovated again, replacing the plastic with ipe (pronounced ee-pay) wood (commonly known as Brazilian walnut).

To the west, many dairies were founded so that the Boynton area became the main milk supplier for Palm Beach County.

[5]: 7–8  The 1928 Okeechobee hurricane in particular caused significant impacts, destroying 46 homes and 18 buildings,[14] including a church, a hotel, and the town hall.

[5]: 8  Additionally, the storm damaged 255 homes and 34 buildings,[14] including the high school, where 15 people suffered injuries after auditorium roof collapsed.

[5]: 8  The Boynton town government faced financial struggles in the aftermath of the 1928 hurricane and during the Great Depression, but received some assistance from the Florida Legislature and negotiated with bondholders for additional debt relief.

[5]: 8  The decade also marked beginning of the construction of Interstate 95 through the city (completed in 1977),[5]: 42–43  the westward expansion of Boynton Beach Boulevard in 1962,[16] the southward extension of Congress Avenue in 1966.

[17] Additionally, residential projects such as the large Hampshire Gardens, Leisureville, and Sterling Village sprang up, causing further growth and economic development.

First, Motorola opened a new paging plant in the city in 1983,[5]: 43  although the complex closed in 2004, about 10 years after its peak, when the facility employed approximately 3,500 people.

[19] Each of these factors attracted more businesses to the area and generated rapid population increases in the city's western suburbs.

[5]: 43 Hurricane Wilma struck Boynton Beach on October 24, 2005, causing widespread damage to homes and businesses.

A high school biology and chemistry teacher, Penserga was sworn into office by State Attorney Dave Aronberg.

A gang-related shooting that resulted in a death at the city's popular Boynton Beach Mall on Christmas Eve of 2006 caught the national attention on many news networks, such as CBS.

[23] On January 27, 2012, Mayor Jose Rodriguez was suspended from office by the state governor for trying to influence a police investigation into his personal affairs.

In addition to Boynton Beach, the historical society also maintains materials relevant to the histories of Briny Breezes, Gulf Stream, Hypoluxo,[45] Lake Worth Beach,[46] Lantana, Manalapan, and Ocean Ridge, as well as areas from the city's western boundaries to U.S. Route 441.

[53] Boynton Beach commissioned a mural showing three of its firefighters, unveiled in 2020, for a window covering at a new fire station.